* Package name : tvb-gdist Version : 1.5.5 Upstream Author : umar haruna abdullahi <umarbrowser20@gmail.com> * URL : http://www.thevirtualbrain.org/ * License : (GPL v3.) Programming Lang: (C++, Python.) Description : Compute geodesic distances (This module the building of a cython wrapper around a C++ library for calculating the geodesic distance between points on a mesh) - why is this package useful/relevant? Yes because it will help alot of people - is it a dependency for another package? yes - do you use it? yes - if there are other packages providing similar functionality, how does it compare? No there was no any other package like it - how do you plan to maintain it? By giving it my full time whenever a new version is out - inside a packaging team (check list at https://wiki.debian.org/Teams)? Yes i am planniong to became one - are you looking for co-maintainers? yes but not now - do you need a sponsor? Yes
If this is supposed to be a Python package, then you might want to consider naming it python-gdist. This links to a website about neuroscience. I don't see a link there to this Cython module. I found the package on pypi: https://pypi.org/project/tvb-gdist/ It seems to require the C++ library at http://code.google.com/p/geodesic/ but code.google.com is dead and the package does not seem to be in Debian? Did you file an ITP for that C++ library as well? Is the package still maintained? Could you elaborate and be more precise? Which one? Really? from geopy.distance import great_circle Or how about this one: from GeographicLib import Geodesic, GeodesicLine Both packages (python-geopy and python-geographiclib) are already in Debian. Since this is a Python package it might fit in the Python packaging team: https://salsa.debian.org/python-team/ Thanks! cheers, josch
No it is not a python package just the require library for the core of tvb-framework https://github.com/umarbrowser/tvb-framework <https://github.com/umarbrowser/tvb-framework> Yes is on of their core modules here is it github address https://github.com/umarbrowser/tvb-geodesic Yes all of the remaining packages vb_data tvb_library tvb_framework are their . They added a python wrapped and made small fixes to the original library, to make it compatible with cython because it has MIT license I am going to package it to http://neuro.debian.net and they recommend submitting my to debian and the will sponsor it *TheVirtualBrain* is a framework for the simulation of the dynamics of large-scale brain networks with biologically realistic connectivity. *TheVirtualBrain* uses tractographic data (DTI/DSI) to generate connectivity matrices and build cortical and subcortical brain networks. The connectivity matrix defines the connection strengths and time delays via signal transmission between all network nodes. Various neural mass models are available in the repertoire of *TheVirtualBrain* and define the dynamics of a network node. Together, the neural mass models at the network nodes and the connectivity matrix define the Virtual Brain. *TheVirtualBrain* simulates and generates the time courses of various forms of neural activity including Local Field Potentials (LFP) and firing rate, as well as brain imaging data such as EEG, MEG and BOLD activations as observed in fMRI. https://github.com/umarbrowser/tvb-framework <https://github.com/umarbrowser/tvb-framework> i will look at it but it has the customize library for tvb-framework and i don't think it's in http://neuro.debian.net I will contact them to became one
Hi,
I am Lia Domide, one of the core developers in TVB Project.
Umar has recently joined the team, as part of Google Summer of Code (GSOC 2018) and his task is to package TVB for NeuroDebian, thus he initiated this work with you.
I will try to add some details to the questions raised on these threads.
The packages we want to publish now are 4:
- tvb-gdist
is similar with other geodesic packages. But at the time of our implementation, this was the only one working on meshes with areas both concave and convex, and easy to access for us from Python.
- tvb-data
contains demo data for TVB demos and tests
- tvb-library
this depends on tvb-gdist and tvb-data
holds the core scientific code for TVB, mainly our simulator. It can be used in the python command line without the next package tvb-framework.
is unique by the fact that it does full brain simulations, modeled at a macroscopic level, considering delays in signal propagation
- tvb-framework
depends on tvb-library, adds web GUI, DB storage and a simple workflow configurator
it includes a full cherrypy based web server structure. Thus, it contains minified versions of MatJax, D3, JQuery and Flot libraries.
We refer their licenses only here: https://www.thevirtualbrain.org/tvb/zwei/brainsimulator-requirements <https://www.thevirtualbrain.org/tvb/zwei/brainsimulator-requirements>. Should they licenses be better emphasized?
These 4 packages have their sources on Github under GPLv3 license: https://github.com/the-virtual-brain <https://github.com/the-virtual-brain>
We packed them for Pypi https://pypi.org/user/tvb/ <https://pypi.org/user/tvb/>
and Conta Forge https://conda-forge.org/feedstocks/ <https://conda-forge.org/feedstocks/> (filter after “tvb”)
We also pack TVB_Distribution https://www.thevirtualbrain.org/tvb/zwei/brainsimulator-software <https://www.thevirtualbrain.org/tvb/zwei/brainsimulator-software> which includes Python, TVB and all dependencies in a ready to use package.
We would like, if possible, the same structures as on Pypi to be available for Debian, with as little as possible changes.
It is important, if our packages are published on your repo, that multiple people have rights to maintain them (me included). How can we easily ensure that?
Best Regards,
Ing. <> Lia Domide
Director of Development at Codemart
Str. Petofi Sandor, Nr. 13, Ap. 4
Cluj Napoca, 400610, Romania
Tel: +40 (364) 401158
+40 (744) 580134
Web: <>http://www.codemart.ro <http://www.codemart.ro/>
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